Yuusaku Matsumi has always been able to hear voices no one else can notice. He hears what people whisper to themselves, the murmurs of animals, and the faint rustle of plants. Most tormenting of all are the voices of the dead, which cling to him constantly. As a child, he tried to block them out, shutting his ears against the fear and loneliness embedded in every sound. But one day, far in the distance, he heard something different, a voice filled with sadness but also warmth, the voice of someone who could see the ghosts he could only vaguely perceive. From that moment, he stopped trying to close his ears and began searching for the source of that voice.

Nearly ten years later, now a high school student, Yuusaku finally finds her. Yukari Tokino is a girl who can see the deceased. When she was seven years old, she became gravely ill and nearly died. When she opened her eyes, she found herself in a world transformed, one populated by ghosts and spirits of every kind, some angry, some lost, all lingering with unfinished business. Where Yuusaku hears their voices, Yukari sees their forms. Their abilities complement each other perfectly, allowing them to perceive the whole picture of a ghost's suffering.

The story follows Yukari and Yuusaku as they encounter an endless stream of the inhuman. They meet ghosts who are hurt even after death, spirits who cannot let go of their loves, and lingering souls with regrets that bind them to the living world. Some of the dead are malicious, seeking to frighten or harm, while others are weak and desperate for any help they can receive. Through each encounter, the two teenagers learn fear, sadness, and compassion, growing as human beings by confronting the pain of those who have already crossed over. Their own connection deepens as well, built on the mutual understanding of what it means to live with one foot in the world of the living and one foot among the dead.

The narrative unfolds through a series of episodic encounters, each focusing on a particular ghost or supernatural phenomenon. Yukari, despite the constant terror and sorrow that comes with seeing the dead, remains determined to help them, while Yuusaku supports her by listening to the voices she cannot hear and deciphering the truths the dead cannot directly show. Together, they work to resolve the lingering regrets of the spirits they meet, guiding them toward peace while navigating the ordinary challenges of high school life and their own complicated feelings for one another. The series is structured as a sequel within a larger body of work, following the original Shi to Kanojo to Boku and preceding a further sequel, Shi to Kanojo to Boku Meguru.